STS-93 marked the 95th launch of the Space Shuttle, the 26th launch of Columbia, and the 21st night launch of a Space Shuttle. Eileen Collins became the first female shuttle Commander on this flight. Its primary payload was the Chandra X-ray Observatory. It would also be the last mission of Columbia until March 2002. During the interim, Columbia would be out of service for upgrading, and would not fly again until STS-109. The launch was originally scheduled for 20 July but the launch was aborted at T-7 seconds. The successful launch of the flight occurred three days later.

Three small holes in the liquid hydrogen cooling tubes inside the nozzle on main engine number 3 are visible, the cause of a hydrogen leak during the mission's launch.

During the main engine ignition sequence, a gold pin used to plug an oxidizer post in the Space Shuttle's number three (right) engine came loose and was violently ejected, striking the engine nozzle's inner surface and tearing open three cooling tubes containing hydrogen. These ruptures resulted in a leak downstream of the main combustion chamber. This anomalous event and the automatic response to the leak by the right engine's controller did not violate any launch commit criteria and liftoff proceeded normally. However, approximately five seconds after liftoff, an electrical short disabled the center engine's primary digital control unit, DCU-A, and the right engine's backup unit, DCU-B. The center and right engines continued to operate on their remaining DCU for the rest of powered flight to orbit. The redundant set of DCUs in each engine controller saved Columbia and her crew from potential catastrophe as shutdown of two engines at that point in the flight would have resulted in a very risky contingency abort[1] with no guarantee of success.[2] The electrical short was later discovered to have been caused by poorly routed wiring which had rubbed on an exposed screw head. This wiring issue led to a program-wide inspection of the wiring in all orbiters.

Because of the leak in the right engine, its controller sensed a decrease in power or thrust—measured indirectly as main combustion chamber pressure—since the leaking hydrogen was not being burned in the SSME's two pre-burners or the main combustion chamber.[3] To bring the engine back up to the commanded thrust level, the controller opened the oxidizer values a bit more than normal. The hydrogen leak and increased oxidizer consumption resulted in the right engine deviating from the desired oxygen/hydrogen mixing ratio of 6.03 and running hotter than normal due to the mixture being closer to the stoichiometric ratio of 8:1. The increased oxidizer consumption during ascent resulted in a premature shutdown of all three engines near the end of the projected burn due to low liquid oxygen level sensed in the External Tank. Though the premature shutdown resulted in a velocity 15 ft/s lower than targeted,[4] the vehicle safely achieved its intended orbit and completed the mission as planned. This incident brought on a maintenance practice change which required damaged oxidizer posts to be removed and replaced as opposed to being intentionally plugged, as was the practice beforehand.

Three days previously, in the first launch attempt, the launch was stopped at T-0:07 seconds, just prior to the SSMEs' ignition sequence, due to a senior console operator manually triggering a cutoff in the countdown. It was later determined that the console operator, monitoring the hydrogen gas concentration in the Space Shuttle's aft compartment where the three SSMEs are located, was fooled by the gas detector's purge cycle which generated a dangerously high, but spurious, reading in the last seconds of the countdown.[5]

The primary objective of the STS-93 mission was to deploy the Chandra X-ray Observatory (formerly the Advanced X-ray Astrophysics Facility) with its Inertial Upper Stage booster. At its launch, Chandra was the most sophisticated X-ray observatory ever built. It is designed to observe X-rays from high energy regions of the universe, such as hot gas in the remnants of exploded stars.

The Shuttle Ionespheric Modification with Pulsed Local Exhaust (SIMPLEX) payload activity researched the source of Very High Frequency (VHF) radar echoes caused by the orbiter and its OMS engine firings. The Principal Investigator (PI) used the collected data to examine the effects of orbital kinetic energy on ionospheric irregularities and to understand the processes that take place with the venting of exhaust materials.

The Southwest Ultraviolet Imaging system (SWUIS) was based around a Maksutov-design ultraviolet (UV) telescope and a UV-sensitive, image-intensified Charge-Coupled Device (CCD) camera that frames at video frame rates. Scientists can obtain sensitive photometric measurements of astronomical targets.

The objective Gelation of Sols: Applied Microgravity Research (GOSAMR) experiment was to investigate the influence of microgravity on the processing of gelled sols. In particular, the purpose was to demonstrate that composite ceramic precursors composed of large particulates and small colloidal sols can be produced in space with more structural uniformity.

The focus of the Space Tissue Loss – B (STL-B) experiment was direct video observation of cells in culture through the use of a video microscope imaging system with the objective of demonstrating near real-time interactive operations to detect and induce cellular responses.

The Shuttle Amateur Radio Experiment (SAREX-II) demonstrated the feasibility of amateur short-wave radio contacts between the shuttle and ground-based amateur radio operators. SAREX also served as an educational opportunity for schools around the world to learn about space by speaking directly to astronauts aboard the shuttle via amateur radio.

The EarthKAM payload conducted Earth observations using the Electronic Still Camera (ESC) installed in the overhead starboard window of the Aft Flight Deck.

The Plant Growth Investigations in Microgravity (PGIM) payload experiment used plants to monitor the space flight environment for stressful conditions that affect plant growth. Because plants cannot move away from stressful conditions, they have developed mechanisms that monitor their environment and direct effective physiological responses to harmful conditions.

The Commercial Generic Bioprocessing Apparatus (CGBA) payload hardware allows for sample processing and stowage functions. The Generic Bioprocessing Apparatus – Isothermal Containment Module (GBA-ICM) is temperature controlled to maintain a preset temperature environment, controls the activation and termination of the experiment samples, and provides an interface for crew interaction, control and data transfer.

The Micro-Electrical Mechanical System (MEMS) payload examines the performance, under launch, microgravity, and reentry conditions of a suite of MEMS devices. These devices include accelerometers, gyroscopes, and environmental and chemical sensors. The MEMS payload is self-contained and requires activation and deactivation only.

The Biological Research in Canisters (BRIC) payload was designed to investigate the effects of space flight on small arthropod animals and plant specimens. The flight crew was available at regular intervals to monitor and control payload/experiment operations.

Columbia's landing at Kennedy Space Center marked the twelfth night landing in the Shuttle program's history. Five had been at Edwards Air Force Base in California and the rest KSC. To date, there had been 19 consecutive landings at KSC and 25 of the last 26 had been there.

In 2001, Coin World reported the revelation (via a FOIA document request) that the Mint had struck 39 examples of the 2000 Sacagawea dollar in gold in June 1999 at the West Point Mint. The planchets came from specially prepared ½ troy-oz $25 American Gold Eagle Bullion Planchets. Why they were struck is not known; speculation is that this was an attempt by the mint to offer "Premium" collectibles in conjunction with the newly released Sacagawea dollar in 2000.

Twenty-seven were soon melted and the remaining 12 were on board Space Shuttle Columbia for the July 1999 STS-93 mission. Two examples then popped up at two separate events; one during a Private Congressional Dinner in August 1999, and another example at the Official First-Strike ceremonies in November. The coins remained at Mint Headquarters under lock and key until they were transferred in 2001 to Fort Knox. The strikes are considered to be illegal due to the Coinage regulations in place.

In 2007, the Mint announced [1] it would for the first time publicly display the 12 space-flown gold dollars at the American Numismatic Association's World's Fair of Money in Milwaukee, WI.

Sleeping shuttle astronauts were often awakened with a short piece of music, a tradition that apparently began during Apollo 15.[7] Each track was specially chosen, sometimes by their families, and usually had a special meaning to an individual member of the crew, or was applicable to their daily activities.[7][8]